Interesting photos (albeit, a bit too tiny for me to see well), but there's something missing from your antenna that mine had!
You see, there's a short fin-like antenna that mine had mounted to the pc board, it looked like either an FM-diversity antenna, or perhaps the antenna for remote start.
In any case, my SR5 had the non-entune radio and the triple coax plug under the headliner only had one connecter installed, so neither of the two antennas were connected to the system.
Anyways, the reason why the housing is so tall is because that diversity antenna fits all the way to the top of the fin.
Not sure where I put the guts from mine, as I replaced it with the stock Pioneer gps antenna inside the housing and mounted it all back on the vehicle.
Oh yeah, as for covering that hole up for good, just get a plastic plug, something like this one:
Then get some clear bra material, around a 2 or 3 square inch piece (just ask for a small piece from any tint shop that does clear bras, I'm sure they'll just give it to you for free) and place it directly over the plug and the roof!
No water should get it and its completely removable without a disaster of adhesive or damaged paint, and it should last many years on the roof without falling apart. That area is NOT where I would want a water leaking into the vehicle!